1W25

RESPONSE REGULATOR PLED IN COMPLEX WITH C-DIGMP

Structural Biology Knowledgebase: 1W25 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.210

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1W25

Classification: SIGNALING PROTEIN

Total Structure Weight: 104344.27

Macromolecule Entities
Molecule Chains Length Organism Details
STALKED-CELL DIFFERENTIATION CONTROLLING PROTEIN A, B 459 Caulobacter vibrioides Gene Name(s): pleD CCNA_02546

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
C2E
Query on C2E

A, B 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)- 3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro- 2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine- 2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin- 6-one)
c-di-GMP, Cyclic diguanosine monophosphate (Synonym)
C20 H24 N10 O14 P2
PKFDLKSEZWEFGL-MHARETSRSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, B MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.239
  • R-Value Work: 0.210
  • Space Group: P 42 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 135.87 α = 90.00
b = 135.87 β = 90.00
c = 169.25 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-06-28
  • Released Date: 2004-11-18
  • Deposition author(s): Chan, C., Schirmer, T., Jenal, U.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: Compliance with PDBx exchange dictionary V4